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- PDB-1uis: The 2.0 crystal structure of eqFP611, a far-red fluorescent prote... -

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Basic information

Entry
Database: PDB / ID: 1uis
TitleThe 2.0 crystal structure of eqFP611, a far-red fluorescent protein from the sea anemone Entacmaea quadricolor
Componentsred fluorescent protein FP611
KeywordsLUMINESCENT PROTEIN
Function / homology
Function and homology information


Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETIC ACID / Red fluorescent protein eqFP611
Similarity search - Component
Biological speciesEntacmaea quadricolor (sea anemone)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPetersen, J. / Wilmann, P.G. / Beddoe, T. / Oakley, A.J. / Devenish, R.J. / Prescott, M. / Rossjohn, J.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The 2.0A crystal structure of eqFP611, a far-red fluorescent protein from the sea anemone Entacmaea quadricolor
Authors: Petersen, J. / Wilmann, P.G. / Beddoe, T. / Oakley, A.J. / Devenish, R.J. / Prescott, M. / Rossjohn, J.
History
DepositionJul 21, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: red fluorescent protein FP611
B: red fluorescent protein FP611
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8286
Polymers52,6282
Non-polymers2004
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-50 kcal/mol
Surface area18420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.935, 77.935, 327.472
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein red fluorescent protein FP611


Mass: 26314.053 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entacmaea quadricolor (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ISF8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: PEG 8000, sodium acetate, calcium acetate, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
126 mg/mlprotein1drop
211.5 %PEG80001reservoir
30.1 %sodium acetate1reservoirpH4.3
40.2 Mcalcium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 20, 2003
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 140379 / Num. obs: 137625 / % possible obs: 96 % / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.07 Å / % possible all: 79.7
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 37625 / % possible obs: 91.2 % / Redundancy: 3.6 % / Num. measured all: 134722 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 79.7 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2526 1514 RANDOM
Rwork0.2135 --
all0.2135 --
obs0.2526 134722 -
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3592 0 2 293 3887
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 4 % / Rfactor Rfree: 0.253 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.007
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.37
X-RAY DIFFRACTIONdihedral_angle_d
X-RAY DIFFRACTIONdihedral_angle_deg26.03
X-RAY DIFFRACTIONimproper_angle_d
X-RAY DIFFRACTIONimproper_angle_deg0.81

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